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ENVO brings structure to biological “environments”

New tool aims to help life science researchers formalize naming conventions for the environments they study. The Science: Biological and biomedical research is increasingly referencing and compiling data from environmental samples, leading to a growing need for a formal and standardized approach to describing those environments. The Environment Ontology (ENVO; www.environmentontology.org) is a community-led, open-access… [Read More]

Out with the old, in with the new, improved Genome Portal

The newest iteration of the DOE Joint Genome Institute’s and analytical tools sports improved user interface and infrastructure. The Science: The DOE Joint Genome Institute’s massive genomic database and data management system, the Genome Portal (http://genome.archive.jgi.doe.gov), has recently been upgraded with a more robust infrastructure to manage the torrent of genomic data available and a… [Read More]

Surprising finds in a rare plant’s mitochondrial genome

Rare and ancient plant gobbles up entire mitochondria from other plants and holds onto them for eons. The Science: One of the oldest flowering plants, Amborella trichopoda, split off from the lineage of other flower plants about 200 million years ago. Analysis reveals that it has a record-setting amount of foreign DNA in its mitochondria,… [Read More]

One big family: Understanding the Polyporales phylogenetic and phylogenomic trees

Looking at a combination of whole genomes and gene databases suggests a new way to examine this fungus family tree. The Science: Researchers reviewed 10 currently available whole genomes, comparing them to known gene datasets. They reported family trees for several taxonomic subgroupings called clades. They also analyzed several single-copy genes to assess them for… [Read More]

Fungi and plants working hand-in-hand

Genomic analysis of an ancient companion of plants shows expanded genes for phosphorus fixation and cell-to-cell communication The Science: More than two thirds of the world’s plants depend on arbuscular mycorrhizal fungi (AMF, also called glomeromycota) because of their ability to fix phosphorus. By analyzing the genome of one AMF, Rhizophagus irregularis (formerly Glomus intraradices),… [Read More]

An insider’s view of bacterial assembly line

A combination of time-lapse fluorescence and transmission electron microscopy reveals how cyanobacteria put together an essential component The Science Cyanobacteria use carboxysomes to make their own energy by “fixing” carbon from carbon dioxide from ocean waters and other aquatic and terrestrial habitats. After deleting the genes cyanobacteria need to build carboxysomes, researchers introduced fluorescent-tagged components… [Read More]

Monkeying around with gene shuffling

The iconic monkey flower’s genome harbors “hot spots” of genetic exchange The Science By analyzing the genomes of a wild population of Mimulus guttatus, also known as the monkey flower, researchers were able to pinpoint “hot spots” in the plant’s DNA code (http://www.archive.jgi.doe.gov/News/news_13_11_18.html with high rates of gene-shuffling recombination. They also provided a reference genome… [Read More]

On the hunt for industrial enzymes

Researchers mined DOE JGI’s database of fungal genomes for candidate enzymes for use in a variety of industrial processes. The Science By screening genomes of fungi made publicly available by the DOE Joint Genome Institute researchers identified new versions of enzymes called lipases and sterol esterases. To further study the most promising enzymes, they created… [Read More]

New tool helps find gene markers in microorganisms

Researchers have devised a novel method to exploit relationships between bacteria and archaea for a new set of gene markers The Science The researchers developed a new way to identify gene markers in bacteria and the primitive microorganisms classified in the kingdom known as Archaea. Dubbed, PhyEco (for phylogenetic and phylogenetic ecology) this strategy can… [Read More]

Lost in symbiosis: genes dropped in piggy-backing bacterial strain

A genome comparison of two strains of a bacterium reveals gene loss as a result of a symbiotic relationship with a protist host. The Science The researchers sequenced the complete genome for a symbiotic strain of the bacterium, Polynucleobacter necessarius. They then compared the symbiont’s genome with the free-living strain in order to understand how… [Read More]